ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2022-10-06T21:29:54+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/232download symlink finished without error, but no data is available2022-10-06T21:29:54+02:00Gerald Salingerald.salin@inra.frdownload symlink finished without error, but no data is availablein case the analyze name contains some special characters, the output folder and/or the symbolic links can't be created :
mkdir -p -m 755 /outputFolder/Analyse_Demultiplexed_subreads_**(**bam**)**.XXX ;
ln -s /inputFolder/file.xml /outp...in case the analyze name contains some special characters, the output folder and/or the symbolic links can't be created :
mkdir -p -m 755 /outputFolder/Analyse_Demultiplexed_subreads_**(**bam**)**.XXX ;
ln -s /inputFolder/file.xml /outputFolder/file.xml;
avoid these characters in the names of run/analysis/projects or replace them when creating the symlinksV3.4https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/227[ont_qc] Change end of sequencing report file2022-05-11T10:29:03+02:00Jules Sabban[ont_qc] Change end of sequencing report fileNanopore has change the end of sequencing report file format from PDF to HTMLNanopore has change the end of sequencing report file format from PDF to HTMLV3.3Jules SabbanJules Sabbanhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/225[Purge] Do not purge the hidden runs and analyses2022-04-26T14:00:23+02:00Romain Therville[Purge] Do not purge the hidden runs and analysesHidden runs and analyzes should be removed from the purge process.
(They will be removed semi-manualy.)Hidden runs and analyzes should be removed from the purge process.
(They will be removed semi-manualy.)V3.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/224Project page : Remove the "Raw data and analysis results use xxx"2022-04-26T14:00:49+02:00Romain ThervilleProject page : Remove the "Raw data and analysis results use xxx"This part of the page is computed on the fly, and does not exclude hidden elements. It can be removed.This part of the page is computed on the fly, and does not exclude hidden elements. It can be removed.V3.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/219Error when updating the database, table tx_nG6_result2022-01-27T17:41:01+01:00Romain ThervilleError when updating the database, table tx_nG6_resultWhen trying to update some filepaths, I made the following mistake:
```
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/data_get/', '/data_seqoccin/');
```
Instead of:
```
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/dat...When trying to update some filepaths, I made the following mistake:
```
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/data_get/', '/data_seqoccin/');
```
Instead of:
```
UPDATE tx_nG6_result
SET rvalue = REPLACE(rvalue, '/data_get/', '/data_seqoccin/')
WHERE analyze_id = 77699;
```
Result:
All the analysis filepaths were wrong for projects in the longterm_get space.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/217"In days, your data will be deleted." in the purge alert mail2022-01-05T14:31:33+01:00Romain Therville"In days, your data will be deleted." in the purge alert mailThe delay in days should appear in the alert mail.The delay in days should appear in the alert mail.https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/216No space_id filter in Administration->Mail obsolete project->Filter on space2022-01-05T14:31:46+01:00Romain ThervilleNo space_id filter in Administration->Mail obsolete project->Filter on spaceIn the drop-down menu, no option is available:
![ng6_bug](/uploads/47ad79eefd6ce3aaa030751cddf06d7e/ng6_bug.png)In the drop-down menu, no option is available:
![ng6_bug](/uploads/47ad79eefd6ce3aaa030751cddf06d7e/ng6_bug.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/214add a link to the reinit password interface2021-10-12T08:47:06+02:00Gerald Salingerald.salin@inra.fradd a link to the reinit password interfaceV3.3Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/213upgrade to typo3 v102021-10-12T08:47:15+02:00Gerald Salingerald.salin@inra.frupgrade to typo3 v10V3.3Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/211Jflow issues2022-11-30T15:59:30+01:00Romain ThervilleJflow issuesLately, we have encountered a lot a failed processes on nG6, and they all seem to revolve around jflow.
I'll put in the issue every jflow error found on ng6.Lately, we have encountered a lot a failed processes on nG6, and they all seem to revolve around jflow.
I'll put in the issue every jflow error found on ng6.V4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/206Login / logout issues2021-05-27T14:45:45+02:00Romain ThervilleLogin / logout issuesAfter a first login, login out or getting disconnected results in a "bad password" error blocking any other connection, with any user.
Clearing the cache, history or cookies doesn't resolve the problem.
It is specific to the browser, ope...After a first login, login out or getting disconnected results in a "bad password" error blocking any other connection, with any user.
Clearing the cache, history or cookies doesn't resolve the problem.
It is specific to the browser, openning a new one allows to connect one user, once.
(Maybe restarting the entire computer works, I haven't tried yet.)V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/204smarty deprecation warnins2021-05-04T11:48:23+02:00Gerald Salingerald.salin@inra.frsmarty deprecation warninsin backend error viewer :
Core: Error handler (FE): PHP Runtime Deprecation Notice: Function create_function() is deprecated in /usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8/ui/nG6/res/smarty/libs/Smarty.class.php line 742
Core: Er...in backend error viewer :
Core: Error handler (FE): PHP Runtime Deprecation Notice: Function create_function() is deprecated in /usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8/ui/nG6/res/smarty/libs/Smarty.class.php line 742
Core: Error handler (FE): PHP User Notice: function call 'assign_by_ref' is unknown or deprecated, use 'assignByRef' in /usr/local/bioinfo/src/ng6_sources/ng6-V3.2.8/ui/nG6/res/smarty/libs/sysplugins/smarty_internal_data.php line 79V3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/203Download by URL gives wrong URLs2021-04-30T20:45:23+02:00Gerald Salingerald.salin@inra.frDownload by URL gives wrong URLs![image](/uploads/8ba8b139a78f25f52d2e4ea6538f3916/image.png)
should be https://ng6.toulouse.inra.fr**/fileadmin/dat**a_shortterm/run/XXX/XXXXGMC_L001_R1.fastq.gz![image](/uploads/8ba8b139a78f25f52d2e4ea6538f3916/image.png)
should be https://ng6.toulouse.inra.fr**/fileadmin/dat**a_shortterm/run/XXX/XXXXGMC_L001_R1.fastq.gzV3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/202ng6 interface slow2021-04-30T20:13:17+02:00Gerald Salingerald.salin@inra.frng6 interface slowNG6 run view quite long to display clicking on a project in project list view, til we got a blank page
Activating the debug preset in typo3 (https://ng6.toulouse.inra.fr/typo3 > Settings > Configuration Presets > Debug settings > Custom...NG6 run view quite long to display clicking on a project in project list view, til we got a blank page
Activating the debug preset in typo3 (https://ng6.toulouse.inra.fr/typo3 > Settings > Configuration Presets > Debug settings > Custom configuration [Active] : BE=1, FE=1, devIPMask=*, displayErrors=1, systemLogLevel=0
refreshing the view displays the error :
Fatal error: Allowed memory size of 2147483648 bytes exhausted (tried to allocate 1743296768 bytes) in /var/www/html/ng6/typo3conf/ext/typo3db_legacy/Classes/Database/DatabaseConnection.php on line 503
Increasing memory_limit in php.ini solved for some time, but Fatal error: Allowed memory size of 2147483648 bytes exhausted (tried to allocate 1743296768 bytes) in /var/www/html/ng6/typo3conf/ext/typo3db_legacy/Classes/Database/DatabaseConnection.php on line 503
I did not found a way to display sql queries, so I added file_put_contents("/var/www/html/ng6/typo3temp/sql.log", $query."\n",FILE_APPEND);
in /var/www/html/ng6/typo3conf/ext/typo3db_legacy/Classes/Database/DatabaseConnection.php > query function
while refreshing the page, output SQL log :
> nG6_project_analyze.analyze_id WHERE tx_nG6_project.uid=1700
> SELECT * FROM tx_nG6_view_project_run WHERE project_id = 1700
> SELECT * FROM tx_nG6_view_project_run_analyze WHERE project_id = 1700
> SELECT * FROM tx_nG6_view_project_analyze WHERE project_id = 1700
> SELECT project_id , count(*) AS count FROM tx_nG6_view_project_run WHERE project_id = 1700 GROUP BY project_id
> SELECT project_id , count(*) AS count FROM tx_nG6_view_project_run_analyze WHERE project_id = 1700 GROUP BY project_id
> SELECT project_id , count(*) AS count FROM tx_nG6_view_project_analyze WHERE project_id = 1700 GROUP BY project_id
> SELECT * FROM tx_nG6_view_project_user
in phpMyAdmin :
SELECT count(*) FROM tx_nG6_view_project_user > 13619506!!!!!!!!!!!!
SELECT * FROM `fe_rights_levels` > 8911!!! whereas we should only have 3 records
refreshing https://ng6.toulouse.inra.fr/projects?tx_nG6_pi1[project_id]=1700 > 2 more records in fe_rights_levels
DELETE FROM `fe_rights_levels` where uid > 3 : refreshing https://ng6.toulouse.inra.fr/projects?tx_nG6_pi1[project_id]=1700 > the page loading is fast
but 2 more records inserted in fe_rights_levels
![image](/uploads/88e304647f722386078feb20ed52b912/image.png)V3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/200allow to display all entries of a datatable in an analysis2021-04-28T16:30:55+02:00Gerald Salingerald.salin@inra.frallow to display all entries of a datatable in an analysisV3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/199update links2021-04-28T14:46:19+02:00Gerald Salingerald.salin@inra.frupdate linkswith the new typo3 version, links are human readable :
change the index.php?id=XX&WWWWWWW with the corresponding page slug in the source
and have to create redirects in apache for those who access the old linkswith the new typo3 version, links are human readable :
change the index.php?id=XX&WWWWWWW with the corresponding page slug in the source
and have to create redirects in apache for those who access the old linksV3.2.8.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/198upgrade to run under typo3 v92021-04-28T18:58:29+02:00Gerald Salingerald.salin@inra.frupgrade to run under typo3 v9V3.2.8Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/196mail method : some people does not receive mails sent by ng6-slurm2021-04-28T18:59:38+02:00Gerald Salingerald.salin@inra.frmail method : some people does not receive mails sent by ng6-slurmhttps://ariane.inrae.fr/block/?id=ariane_ticket&table=incident&sys_id=96e56e891bdfec102c571176bd4bcb76https://ariane.inrae.fr/block/?id=ariane_ticket&table=incident&sys_id=96e56e891bdfec102c571176bd4bcb76V3.2.8Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/195multiple CC in purge emails2021-03-25T14:28:31+01:00Gerald Salingerald.salin@inra.frmultiple CC in purge emails![image](/uploads/c6e10d7c41b8932e146e5218aab123fe/image.png)
the headers array given to the sent email is populated in each loop of the foreach block![image](/uploads/c6e10d7c41b8932e146e5218aab123fe/image.png)
the headers array given to the sent email is populated in each loop of the foreach blockV3.2.7.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/191[ont_qc] Add {} for bash variable of more than one number2021-02-15T10:45:27+01:00Roxane Boyer[ont_qc] Add {} for bash variable of more than one numberWe had an issue recently where the command would not be correctly interpreted :
```
ng6@node103 /work/ng6/jflow/work/ont_qc/wf007676 $ cat /work/ng6/jflow/work/ont_qc/wf007676/.working/7c6b4a7d6d/_Stash/0/0/0/w0000021
#!/bin/sh
module...We had an issue recently where the command would not be correctly interpreted :
```
ng6@node103 /work/ng6/jflow/work/ont_qc/wf007676 $ cat /work/ng6/jflow/work/ont_qc/wf007676/.working/7c6b4a7d6d/_Stash/0/0/0/w0000021
#!/bin/sh
module load bioinfo/seqkit-v0.9.3
/usr/local/bioinfo/SeqKit/seqkit-v0.9.3/seqkit stats --all $1 $2 $3 $4 $5 $6 $7 $8 $9 $10 $11 $12 $13 $14> $15
```
Was just adding a number behind an argument. Exemple, if $1 contains "unclassified.fastq.gz", then echo $15 will give : "unclassified.fastq.gz5".
We never noticed this issue before because we never had multiplexed run with more than 8 sample. To correct this issue, you should put the variable in this format : ${15}, like this :
`/usr/local/bioinfo/SeqKit/seqkit-v0.9.3/seqkit stats --all ${1} ${2} ${3} ${4} ${5} ${6} ${7} ${8} ${9} ${10} ${11} ${12} ${13} ${14}> ${15}`
Thank you for your help :unicorn:V3.2.8Audrey GibertAudrey Gibert